R Observatory: Metrics for tracerer version 2.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tracerer

2.2.4Package record

Tracer from R

2packages dependsuggested by 3

5.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Richèl J.C. BilderbeekCRAN page ↗GitHub ↗Website ↗Issues ↗rOpenSci review: issue 209 ↗

'BEAST2' (https://www.beast2.org) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (https://github.com/beast-dev/tracer/) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("tracerer", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/tracerer")

Development version from ropensci/tracerer. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-tracerer

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-tracerer

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-tracerer

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.4

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 35 (1 internal)includes a package overview page
Examples that run: 100%22 run in a plain check
Exported functions with examples: 71%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (1)

tracerer versus Tracer demo HTML

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #7,815 · ~15/day · ~457/mo

Releases R versions

Daily download trend is not available in this view yet.

37830 days

1.2K90 days

5.5K1 year

Compare downloads with other packages →

Also on395 r2u1 autocran99 c2d4u

How downloads are counted

Repository

ropensci/tracerer ↗Organization: ropensci

8Stars

3Forks

0Open issues

0Open PRs

20Releases

429Commits

5Commit identities

rr-packagerstats

License file reads as GPL-3.0 · 429 commits · Last activity 2026-08-13 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2021-03-04 · 82026-07-07 · 8

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ropensci/tracerer on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Coverage (1)

Coverage reporting

Research and citation (2)

CITATION.cffcodemeta.json

Show all practicesHide 1 practice

Lint, format, editor (2)

Lint workflowRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing tracerer adds 2 packages (2 with compiled code, 2.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, jsonlite 1.0 MB.

Depends (0)

none

Imports (2)

jsonlite Rcpp

LinkingTo (1)

Rcpp

Suggests (8)

ape ggplot2 knitr phangorn rappdirs rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

Depends 1 · Imports 1

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

babette nodeSub

Suggests, most downloaded first

beastier mauricer mcbette

How these are counted

Code & Tests

People & History

People (4)

Richèl J.C. Bilderbeek

Author, Maintainer · added in 2.0.1

Roberto Villegas-Diaz

Contributor · added in 2.2.4

Joëlle Barido-Sottani

Reviewer · added in 2.0.1

Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

David Winter

Reviewer

David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

Maintainer since 1.5.1 (2018)

Listed in earlier versions (2)

Joelle Barido-Sottani

no longer listed · 1.5.1

Richel J.C. Bilderbeek

no longer listed · 1.5.1

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.4Latest
record
2026-03-02 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.2.3
record
2023-09-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.2.2
record
2021-05-30 · diff ↗ ·
added 5 exports
calc_geom_mean, calc_mode, check_trace, get_tracerer_tempfilename, parse_beast_tracelog_file
R
R 4.1.0 released · 2021-05-18
2.1
record
2020-05-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.2
record
2019-12-02 · diff ↗ ·
added 1 export
is_trees_file
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-03-01
2.0.1
record
2019-03-01 · diff ↗ ·
added 3 exports
count_trees_in_file, save_beast_estimates, save_beast_trees
archivedRemoved from CRAN
2018-10-30
policy violation Checking creates 'tmp_tracerer_rprof' in home

Show 2 earlier eventsHide 2 earlier events

1.5.1
record
2018-10-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-30
Total releases: 7 / 8 yrs
License: GPL-3 OSI
Download size: 1.2 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("tracerer")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.13032.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for tracerer version 2.2.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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